Got the fuse box in place today and started laying out the interior harness's, The dash harness's and engine bay are easy enough to deal with since they pretty much sit in the same place for the MJ as the XJ. However the body harness is a little different, today I placed it in the cab as is and didn't like how it was working out since the harness was meant to work with the 4 door XJ.
I stripped out the rear door wiring for the courtesy light and power windows, as well as the rear overhead light wiring. I still need to pull out the speaker wiring, rear wiper, and defrost wiring. I also then need to figure out how to arrange the remainder of the rear light wiring. the plugs used at the back of the XJ behind the spare tire will reach part way, but are not weatherproof connectors so they really shouldn't be used under the bed as-is.
I stripped the harness wrap bare so I could move some things around, but I am attempting to avoid a million splices in the harness.